fix: isolate citation registries per pipeline

[ump45nose]

Summary

• isolate citation state behind a unique registry ID for each LightResearch pipeline run
• pass that ID through the generated tool metadata and release the registry when the pipeline completes
• add a focused regression test that interleaves two runs and verifies their citation counters remain independent

Root cause

init_citation_registry() reset a class-level dictionary shared by every request. Starting a second pipeline therefore erased the first pipeline's in-progress citation mappings.

Validation

• pytest -p no:cacheprovider tests/test_citation_registry.py -q
• ultrarag build examples/demos/LightResearch.yaml
• generated MCP metadata smoke for init, assign, and clear tool contracts
• ruff check --select I,F,E9 tests/test_citation_registry.py
• ruff check --select I servers/custom/src/custom.py

Fixes #394

[ump45nose]

@xhd0728 This focused LightResearch concurrency fix is ready for review. It scopes citation registries by pipeline-run ID, carries that ID through generated tool metadata, and releases the registry on completion; the regression interleaves two runs and verifies independent counters. The focused pytest, pipeline build, MCP metadata smoke, and targeted Ruff checks pass. Since you maintain and review servers/custom/src/custom.py and the related demo pipelines, could you take a look when convenient?